GATKSupportTeam

Funcotator IllegalArgumentException

4

This request was created from a contribution made by Jay Singh on May 09, 2020 12:47 UTC. Link: https://gatk.broadinstitute.org/hc/en-us/community/posts/360062649991-java-lang-IllegalArgumentException-Invalid-interval-Contig-chr1-start-9-end-10464 -- Can you please provide a) GATK version used - **gatk-4.1.7.0**...

CNNScoreVariants crashes with java.lang.NullPointerException

5

Looks like this java.lang.NullPointerException is from an environment set up issue. This request was created from a contribution made by Jordi Maggi on April 25, 2022 09:25 UTC. Link: [https://gatk.broadinstitute.org/hc/en-us/community/posts/5574426055963-CNNScoreVariants-crashes-with-java-lang-NullPointerException](https://gatk.broadinstitute.org/hc/en-us/community/posts/5574426055963-CNNScoreVariants-crashes-with-java-lang-NullPointerException)...

AnalyzeCovariates no option for second recalibration table

3

### Summary In the AnalyzeCovariates documentation, there is mention of the previous GATK3 method to obtain recalibration tables before and after BQSR. There does not seem to be that functionality...

Feature Request - extract Funcotator VCF INFO 'sub-fields'

1

A user on the GATK Forum submitted a request to make the INFO field easier to manipulate through creating a table. At the GATK Office Hours meeting 11/8, we discussed...

Picard FilterSamReads exit codes writing to stdout

2

### Summary A user wrote in to the forum regarding running FilterSamReads through GATK and the output bam file has formatting issues. After they sent in a bug report, I...